Stargate Atlantis: A Matter of Time
by LordApophis155
Summary: Some spooky stuff happens, McKay 'technobabbles' and stuff gets destroyed. The team return from Lantea's mainland to find Atlantis's shield raised with no explination and they can't make radion contact. Spooky. I am aware of some grammar mistake.
1. Chapter 1

**Stargate Atlantis:**

**A Matter of Time**

**Disclaimer:

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**

_I do not own Stargate Atlantis or any of it's related characters. The property of MGM.

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_

**Chapter One**

The sun began to set over the vast rolling ocean as Jumper Three made the return trip to Atlantis. The sun reflected off of the ship casting a rippling reflection in the water below them.  
"I still don't see why I had to come." whined Dr Rodney McKay to anybody that cared to listen, which in this case appeared to be nobody. Realising that nobody was paying him any attention, he continued with his rant, "It's not like I was needed, the drive pods accepted the new modifications perfectly with no trouble, the command interface adapted as I predicted it would." at this Colonel Sheppard felt he should say something to prevent one of Rodney's full blown hissy fits for which he was renowned.

"It was your idea to modify the drive pods to maximize output, Elizabeth wanted you there in case anything went wrong, and I would hardly say that the trip was perfect, what about the sudden drop in altitude at launch?" he asked, glaring at the scientist.

"I fixed it didn't I? And why did I need to stay on the mainland, I could have flown the Jumper back myself and sent one for you later." he said with a tone that indicated he had won against the Colonel, however this was soon deflated as a retort came from Teyla, the teams third member,

"I wished to speak with my people on the mainland, I have not seen them in a long time and Colonel sheppard kindly offered to take me there this morning." she said, hoping to bring an end to the bickering, but she should have known John always wanted the last laugh, to borrow an Earth expression.

"Besides, I've seen you fly a Jumper…" he said with a smirk, Rodney's response was lost to an alarm sounding from the Jumper's control console.

"What did you do?" yelled Rodney, automatically jumping to conclusions, another one of his favourite past times.

"I'm getting the 'Do Not Proceed' signal from Atlantis, according to the sensors, the shields are raised." concern leaked from the Colonel's words, it wasn't like Elizabeth to raise the shields without radioing them first. He slowed the Jumper to a stationary hover just before the shield.

"Rodney, any ideas?" John asked while the scientist tapped madly at his laptop.

"Gimme a minute here." he said, sounding exasperated.

"Perhaps there is a Wraith ship in the area…" suggested Teyla, but in usual fashion Rodney stomped on that theory,

"If there was a Wraith ship in the area they would have cloaked and they wouldn't have done it with out contacting us first." as much as John hated to admit it Rodney was right, for good measure he kept this thought to himself.

"I'm getting sensor telemetry from inside the shield. I think…"

"You think?" remarked Teyla; she found it unusual for Rodney to be uncertain, to his credit he was always certain, even if he turned out wrong.

"According to the readings, Atlantis…well…it's not there." he looked at sheppard, bemused.

"What?!? Rodney I can see the damn city in front of me, how is it not there?" yelled sheppard, his patience growing thinner by the second.

"Could we not just pass through the shield, I have seen Puddle Jumpers do this before?" asked Teyla, feeling out of depth trying to comprehend what Rodney had just said.

"No," McKay answered, "When we did it before the Jumpers own shield was calibrated to the same frequency as Atlantis's shield, allowing it to pass right through. I might be able to do it from here but it will take longer without the correct equipment, not to mention the fact we don't know why the shield is raised, is it so wise to go in there without knowing what's going on?" again John felt the need to keep his agreement with Rodney quite.

"Do it. But before we go storming in we'll try and get more intel first."

Rodney climbed out of his chair a moved into the Jumpers rear compartment and began fiddling with various crystals and wires while John and Teyla shared a concerned look with each other.

An hour passed as Jumper Three now cast an eerie reflection into the ocean by the moonlight as it hovered just before the shield. They had powered down several systems to maintain there position, Rodney had worked out it would use more power returning to the mainland.

"Rodney, how close are you to getting the shields sorted?" yawned John, looking sleepily at McKay.

"Hm? Oh there done, I've been working on a sensor modification to try and…" much to Rodney's annoyance the Colonel cut across him,

"There done? Why didn't you tell me? We're wasting time out here when we could be in there?" he asked McKay who was now giving him the annoyed look he reserved especially for the Colonel.

"If you had let me finish, you would have heard a perfectly rational explanation as to why we aren't in there now." answered McKay, pausing only to continue to foul look the Colonel was getting, "I have been working on a sensor modification which should allow me to work through what ever interference is present, it may even allow us to make radio contact." Rodney finished, slightly calmer than before. "I just need to upload the program into the Jumper's sensor array, shouldn't take long." he muttered, more to himself as he pulled various parts of the Jumper around and plugged in his data tablet. A row of crystals lit up as he did this and began emitting a low hum.

"Good, it's uploading now, sheppard, get us into position above the Jumper bay." the Colonel woke the Jumper and pulled up around the shield dome to the top of the control tower's Jumper bay entry hatch.

"McKay?"

"Hang on, fifteen seconds…now, bring up the HUD." Rodney answered. The holographic HUD appeared on the Jumpers main window.

"Initiating scan." said sheppard, hitting several buttons on the Jumpers console.

"Receiving telemetry." stated Rodney. The HUD displayed nothing but static where there should have been a clear picture of Atlantis. "Are we definitely scanning and getting feedback?"

"Yes," confirmed McKay, "I don't know what's going on, increasing scanner strength, fifty percent." still the HUD only displayed static. "Increasing seventy five percent." this time the HUD showed a scrambled picture, a wire frame map of the city, but still static distorted the image. "Increasing one hundred percent." The image was still not perfect, but clearer. sheppard let McKay worry about the technical jargon being displayed next to the image while he open a radio channel to the control tower;

"Atlantis this is Jumper Three, please respond. Atlantis, this is sheppard do you copy?" only silence answered his radio call. "Rodney, can you get me anymore energy?"

"What? You can't be serious! Look we burnt a lot of energy staying hovered, which the Jumper isn't designed to do…" Rodney stammered as sheppard gave him the look that said, 'I know you can do it McKay', a look he normally gave when he was expecting the impossible, which usually worked, but this time there was no chance. "There is no more power that I can divert without compromising key systems…" the look continued "Highlight the word KEY systems, if you want to get through that shield then there is no more power. That's final." finally sheppard gave up.

"Alright, activate the shield and let's go in." ordered the Colonel.

"John, is that so wise when we do not know the nature of what has happened?" said Teyla, who had been following the convocation silently.

"She's right," said McKay, "I can't make head nor tale of this data, as far as I'm concerned the scanners aren't working, the data goes against all the laws of physics."

"Perhaps we should return to the mainland and attempt to contact the _Daedalus_…" this time sheppard cut her off;

"The _Daedalus_ landed alongside the east pier just before we left this morning, it's under the shield too." said sheppard solemnly.

"Alright, lets get this over with, maybe from that side of the shield I can tale proper readings…activating shield" muttered McKay as sheppard lowered them through the shield and sent the remote access open command to the roof hatch.

"Err, McKay, the roof isn't opening." sheppard stated, glancing at Rodney.

"Damn it, I was afraid of that," he said "I think the number of modifications we've made on this lovely day trip has routed power away from the remote access command; I can't put it right without us being landed."

"Colonel, is there not a flat topped tower just through there, if I am not mistaken it also has and entry hatch?" asked Teyla.

"Excellent, I'll put us down there." the Jumper thudded gently as it touched down on the roof top. "McKay you stay here and work on getting the roof open and those sensor readings, Teyla, you're with me." said sheppard handing her a P-90 and a side arm from the Jumpers stores. Teyla hit the hatch release and listened as the whirring of the gears was ended when the hatch hit the ground.

"Alright," said McKay, "Radio's should work, we're on top of an auxiliary tower, no one from the expedition should be here, I suggest you walk through to the control tower, something may have compromised transporters. Good Luck."

John and Teyla stepped out on to the tower top, a cold brisk wind caught Teyla by surprise, around them the city was dark, which in it's self is strange, normally, by this time of night the lights were on, illuminating the ocean around the city. John headed for the door and forced it open…

McKay sat in his seat in the Jumper at the laptop; he attached a side arm to his holster just in case. I didn't take Rodney long to find an anomaly he recognised…

"Sheppard, Teyla!" he yelled into his radio, "Fall back to the Jumper now, you cannot enter the city!"

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**Ok hope you like, I will update with Chapter Two ASAP.**


	2. Chapter 2

**Stargate Atlantis: **

**A Matter of Time**

**Disclaimer:**

_I do not own Stargate Atlantis or any of its related characters. The property of MGM._

**Chapter Two**

**Eight Hours Previously**

McKay swore under his breath as he pulled bits of crystal and cable out of Jumper Three's control console.

"Gotcha'!" he muttered, as though he had won a personal battle against the delicate crystals. He rammed an interface plug into the console, which lit up, flickered and went out, he glared at the console as though it had done him a personal insult. McKay's cursing was lost to the sound of voices entering the Jumper bay, they seemed to move away from him, this suited him perfectly, there was nothing more irritating than people talking to you when you're trying to talk to you and you're just not listening to them. He ignored them and carried on working on the crystals.

"Rodney?" asked a voice behind him, he recognised it as Dr Zelenka.

"What?" sighed McKay.

"How are the modifications to the Jumpers drive pod coming?"

"They would be coming a lot faster if a certain Czech scientist stopped bothering me." Rodney turned to his fellow scientist and saw he was geared up to go off world. "Where are you going?"

"We're going to M1M-762, a small planet on the very edge of the galaxy, Elizabeth thinks there might be an Ancient outpost there and wants it explored." he said in his soft Czech accent. McKay glared.

"And she chose your team over ours?" asked McKay, "I thought we were first port of call for Ancient outposts?"

"Normally you are but Sheppard suggested you would rather stay here and work on the Jumper modifications." said the scientist with a smirk. Major Lorne came around the side of the Jumper, also geared for off world.

"Ready Doc?" he asked Zelenka.

"Yes Major" he said as the Sergeant in charge of the Jumpers came into view.

"What is this, a house party?" yelled McKay, "Trying to work here!"

"Pre-flights complete on Jumper Five sir, you're cleared for launch." said the Sergeant, blanking McKay completely.

"Thank you Sergeant. Let's go doc." ordered Lorne.

As McKay return to the infuriating crystals, he heard the soft hum of Jumper Five lowering into the gate room.

Half an hour later McKay was done, after several choice curse words, a shower of sparks and three cuts to his forearm later, the drive pod modifications were complete. McKay tapped his radio ear piece,

"Elizabeth, I'm done with the modifications." he said, his tone on of triumph.

"Excellent Rodney, meet Colonel Sheppard and myself in the briefing room to go over the changes. Weir out." McKay sighed as he heaved himself out of the Jumpers chair and walked down the hatch.

"Touch that Jumper, and I will make your life hell!" McKay yelled at the Jumper Sergeant.

"Yes Sir." said the Sergeant.

One short transporter trip later, Rodney arrived in the briefing room and helped himself to coffee and biscuits before joining John and Elizabeth at the table.

"Okay, so Rodney, what, what changes have you made to the Jumpers?" asked Weir, cutting straight to the chase.

"Well, I've input a new command into the Jumpers flight matrix which _should_ allow the Jumper to almost double it's top speed, of course I had to adjust the Jumpers inertial dampeners to compensate for the new speed which _should_ have worked." said McKay with a satisfied smile on his face.

"I heard the word 'should' a lot in that sentence" remarked the Colonel, looking over at McKay.

"Alright,_ will _work. Better?" answered the scientist sarcastically.

"Okay, you're cleared for flight to the mainland." said Elizabeth, stepping in before the Colonel could retort.

"What? Mainland, Why?" questioned McKay.

"Because I'm not risking a modified Jumper off world and Teyla has requested a trip to the mainland, I need you there in case something goes wrong." answered Weir firmly.

"Ronon coming for a hunt?" asked Sheppard.

"No, he's staying, he's bet that he can take on half the _Daedalus_ marine contingent by himself."

"Tell the marines not to loose to badly." warned Sheppard.

Elizabeth laughed as the Gate Technician, Chuck, came into the room,

"Ma'am, flight has just confirmed the _Daedalus_ has landed alongside the east pier."

Fifteen minutes later the team was geared and in the Jumper.

"Flight this is Jumper Three, request permission to launch."

"Jumper Three, this is flight, you are cleared to launch Colonel. Good Luck."

Sheppard eased the Jumper up through the roof hatch and out into the blinding light of Lantea's sun. Whirring came from the back of the Jumper as the drive pods extended on either side of the small ship.

"Right, just give it a minute to alter the command interface to allow for the new speeds…done" said McKay. The Jumper shot forward, until an alarm sounded from the console.

"We're loosing altitude McKay! The port drive pod is not functioning, make that both drive pods!" yelled the Colonel as the ship plummeted toward the ocean. McKay was frantically tapping at his laptop cursing. The hum of energy could be heard as the Jumper began to launch forwards again, skimming the ocean.

"Got it." said McKay, laughing with relief only to be silenced with a glare from his two team mates.

***

**Present Time**

Sheppard ran up the Jumpers hatch and in to the ship as McKay sat looking shocked staring at the readings on his laptop.

"What is it McKay?" asked Sheppard.

"The readings I'm getting from the laptop, I've seen readings like them before at the SGC when we inadvertently dialled a black hole and time began to slow down."

"So you are saying time has slowed down within the city?" asked Teyla looking a Rodney astonished.

"No, I said readings _like_ that at the SGC. These are different. If I'm correct, which I usually am, time inside the city has come to a complete standstill." finished the scientist, pausing for dramatic effect.

"Then how can we still move?" Teyla inquired.

"I…I don't know… but it would explain why the Jumper bay doors wouldn't open, they can't, maybe because we weren't here when it started we're immune. I'll know more once we get to the control room."

"Alright, move out." ordered Sheppard.

They made their way through the deserted auxiliary tower until they reached a bulkhead door. John made to wave his hand in front of the door control only to find it wouldn't open.

"Duh, frozen time." said McKay, "We'll have to wedge it open."

"By us, you mean me?"

"It may surprise you Colonel but I'm not a strong as I look." smirked Rodney.

"Not really, I know it was you that finished the city's doughnut supply." retorted the Colonel, earning him yet another filthy look. The Colonel handed his P-90 to Teyla who stood out the way with Rodney.

"You know they call these things 'bulk heads' for a reason right?" said Sheppard.

"What do you suggest then?" Rodney regretted this almost instantly as Sheppard pulled a block of C4 explosive from one of his vest pockets and attached it to the door.

"Get round that corner there." said the Colonel, indicating the way they had just come. "Fire in the hole!" he said a fire swept through the corridor, blasting the bulkhead.

"I think Elizabeth might be ticked." observed Rodney as John accepted his P-90 from Teyla.

They walked to the control room. For a while they didn't see anyone or anything to support Rodney's theory. Until:

"Whoa!" yelled Rodney as they entered the control tower and saw several expedition members frozen. "There not moving!"

"Very astute Rodney, frozen time ringing any bells?" asked John, rather irritated by the remark.

"Alright, control room, I'll get up stairs and try and work out…wow."

***

**M1M-762:**

**Seven and a Half Hours Previously**

Jumper Five sat in a high orbit around the arid world. Very few stars were visible this far out in the galaxy. Lorne eased the Jumper into a shallow bank so that they were looking down on the world.

"The scan is running now," said Zelenka, "If there's an outpost down there this will find it." Several minutes of nothingness passed until the HUD displayed itself over the view screen.

"I'm picking up one subterranean structure towards the planets equator." said Lorne as he pushed the Jumper through the planets atmosphere.

"Let's see what we've got." said Lorne.

**Ok…Second chapter done…Third on its way. :D**


	3. Chapter 3

**Stargate Atlantis: **

**A Matter of Time**

**Disclaimer:**

_I do not own Stargate Atlantis or any of its related characters. The property of MGM._

**Note From Author:**

_I would like to apologise for the delay in the release of part three (it's been ages :S) but I have been completely swamped recently._

**Chapter Three**

Rodney stood at the top of a sweeping stairway leading into Atlantis's vast embarkation room, but the normally large empty area was filled with a frozen Jumper.

"Sheppard!" yelled the scientist at the sight of the Jumper suspended in mid-air.

"Damn it Rodney I'm right next to you, are you trying to deafen…whoa." exclaimed the Colonel at the odd sight. "What the…"

"John, Rodney, I think I've found something…" shouted Teyla who had made her way to the city's control room and was now examining a console.

"What is it?" asked John, who had run over with Rodney brining up the rear. "What is this console?"

"It's responsible for city defence, shields matrix, biometric sensors etc… although I have never seen it do that." The console, which normally glowed a soft white, like all of Atlantis's control consoles, was now glowing a vivid blood red.

"That can't be good…" said the Colonel.

"Very clever 'Mr Astute', red usually means bad, but what is actually bad is another story entirely. I can try to interface with the city, but I'm not hopeful, from what I can ascertain we can't interface with the consoles, so we only have use of the data here…although, the Jumpers Systems are still active, I might be able to use it's sensors to get more data on what caused this."

"Go." said John, "Me and Teyla will go for a little walk, take a look around."

Rodney left back the way they had come to the tower they had landed on, while John and Teyla descended the steps into the Gate Room toward the frozen Jumper. John placed a foot on the front of the Jumper, as though testing his weight on it, once he was sure he climbed up to look through the view screen into the Jumper. The rear bulkhead was shut, although all four team members were in the cockpit.

Lorne sat at the flight controls, a look of determined concentration on his face.

Zelenka sat in the co-pilots seat, working frantically at a data pad.

A marine was propped up against the closed bulkhead, he appeared to have lost a lot of blood, the fourth team member attended the wounded marine.

"There's a wounded man in there," Sheppard told Teyla, who was examining the rest of the Jumper. "I wonder what's in the back compartment, why is the bulkhead shut?" He wondered aloud.

"Colonel, there's something vibrating in the rear compartment, I can feel it." The Colonel came over to her and placed his hand on the hull of the Jumper.

"Yeah, I feel it to."

***

**M1M-762:**

**Five Hours Previously**

Major Lorne and his team reached the peak of a large ridge that seemed to span for miles around. He clambered with skill over the top, to find him self staring at a large crater. He scanned the craters walls, but there was no sign of a door or access points.

Zelenka soon joined him to look over the crater, he was panting heavily,

"You okay doc'?" he asked the scientist.

"I'm fine…" said Radek, frowning at his scanner and muttering to himself in Czech. "The scanner says the door should be directly in front of us in the opposite wall of the crater…unless…. Major, I think we should head over there."

"There's nothing there Doc'."

"I wouldn't be to sure, my scanners picking up an energy signature consistent with that of a cloak."

"So, it could just be protected?"

"Yes, I think so." said the Scientist.

**Ok, sorry for cutting this chapter short, but I'm working on another project at the moment, as well as other stuff so this has had to take a back seat. :( I'll update ASAP.**


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